Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells

Genomes of the Mouse Collaborative Cross

(2017) Anuj Srivastava et al.   GENETICS

Derivation of ground-state female ES cells maintaining gamete-derived DNA methylation

(2017) Masaki Yagi et al.   NATURE

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

The gestational foundation of sex differences in development and vulnerability

(2017) J.A. DiPietro et al.   NEUROSCIENCE

Sex-specific differences and developmental programming for diseases in later life

(2017) Deepali P. Sundrani et al.   REPRODUCTION FERTILITY AND DEVELOPMENT

Genomes of the Mouse Collaborative Cross

(2017) Anuj Srivastava et al.   GENETICS

Gene Regulation: Stable Noise

(2016) Jonathan R. Chubb   CURRENT BIOLOGY

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation

(2016) Geng Chen et al.   GENOME RESEARCH

Impact of the X Chromosome and sex on regulatory variation

(2016) Kimberly R. Kukurba et al.   GENOME RESEARCH

A childhood acute lymphoblastic leukemia genome-wide association study identifies novel sex-specific risk variants

(2016) Sandeep K. Singh et al.   MEDICINE

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

(2016) Ferdinand von Meyenn et al.   MOLECULAR CELL

The importance of having two X chromosomes

(2016) Arthur P. Arnold et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dosage compensation of the sex chromosomes and autosomes

(2016) Christine M. Disteche   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Escape Artists of the X Chromosome

(2016) Bradley P. Balaton et al.   TRENDS IN GENETICS

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Sexual Dimorphism in Adverse Pregnancy Outcomes - A Retrospective Australian Population Study 1981-2011

(2016) Petra E. Verburg et al.   PLoS One

Widespread DNA hypomethylation and differential gene expression in Turner syndrome

(2016) Christian Trolle et al.   Scientific Reports

Sex-Specific Effects of Testosterone on the Sexually Dimorphic Transcriptome and Epigenome of Embryonic Neural Stem/Progenitor Cells

(2016) Matthew S. Bramble et al.   Scientific Reports

Sex matters to the heart: A special issue dedicated to the impact of sex related differences of cardiovascular diseases

(2015) Hester M. Den Ruijter et al.   ATHEROSCLEROSIS

Genetics of cardiovascular disease: Importance of sex and ethnicity

(2015) Stacey J. Winham et al.   ATHEROSCLEROSIS

GOplot: an R package for visually combining expression data with functional analysis: Fig. 1.

(2015) Wencke Walter et al.   BIOINFORMATICS

Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development

(2015) Robert Lowe et al.   BMC GENOMICS

Cell fate commitment during mammalian sex determination

(2015) Yi-Tzu Lin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Genetic Architecture of Sexual Dimorphism in Humans

(2015) Nichole Rigby et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

(2015) James J Crowley et al.   NATURE GENETICS

Opinion: Sex inclusion in basic research drives discovery: Fig. 1.

(2015) Sabra L. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of whole-genome autosomal differences of DNA methylation between men and women

(2015) Paula Singmann et al.   Epigenetics & Chromatin

Escape from X Inactivation Varies in Mouse Tissues

(2015) Joel B. Berletch et al.   PLoS Genetics

The evolution of sex differences in disease

(2015) Edward H Morrow   Biology of Sex Differences

In Vitro Fertilization Affects Growth and Glucose Metabolism in a Sex-Specific Manner in an Outbred Mouse Model1

(2014) Annemarie Donjacour et al.   BIOLOGY OF REPRODUCTION

The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network

(2014) Edda G. Schulz et al.   Cell Stem Cell

X-chromosome inactivation in development and cancer

(2014) Ronan Chaligné et al.   FEBS LETTERS

Sex Differences in Pediatric Infectious Diseases

(2014) M. Muenchhoff et al.   JOURNAL OF INFECTIOUS DISEASES

Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain

(2014) Bryant M. Schultz et al.   NUCLEIC ACIDS RESEARCH

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

PRDM14: a unique regulator for pluripotency and epigenetic reprogramming

(2014) Fumio Nakaki et al.   TRENDS IN BIOCHEMICAL SCIENCES

Sex-Biased Gene Expression and Sexual Conflict throughout Development: Table 1.

(2014) Fiona C. Ingleby et al.   Cold Spring Harbor Perspectives in Biology

Sex-Dependent Gene Expression in Human Pluripotent Stem Cells

(2014) Daniel Ronen et al.   Cell Reports

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

(2013) Masashi Yamaji et al.   Cell Stem Cell

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

(2013) Gabriella Ficz et al.   Cell Stem Cell

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

Guided by RNAs: X-Inactivation as a Model for lncRNA Function

(2013) John E. Froberg et al.   JOURNAL OF MOLECULAR BIOLOGY

Tsix RNA and the Germline Factor, PRDM14, Link X Reactivation and Stem Cell Reprogramming

(2013) Bernhard Payer et al.   MOLECULAR CELL

The evolutionary causes and consequences of sex-biased gene expression

(2013) John Parsch et al.   NATURE REVIEWS GENETICS

Mouse Phenome Database

(2013) Stephen C. Grubb et al.   NUCLEIC ACIDS RESEARCH

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

(2013) N. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Female Bias in Rhox6 and 9 Regulation by the Histone Demethylase KDM6A

(2013) Joel B. Berletch et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency

(2013) Jamie A. Hackett et al.   Stem Cell Reports

Updated assessment of the prevalence, spectrum and case definition of autoimmune disease

(2012) Scott M. Hayter et al.   AUTOIMMUNITY REVIEWS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

Maps for Changing Landscapes: Viewing Epigenomic Signatures through Differentiation

(2012) Michael Bulger   Cell Stem Cell

Genetic considerations in the patient with Turner syndrome—45,X with or without mosaicism

(2012) Quincy Zhong et al.   FERTILITY AND STERILITY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation

(2012) F. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome

(2012) E. Pessia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex differences in developmental programming models

(2012) Catherine E Aiken et al.   REPRODUCTION

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

(2011) M. Smoot et al.   BIOINFORMATICS

Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome

(2010) Alexandra M Lopes et al.   BMC GENOMICS

Sexual Dimorphism in Mammalian Autosomal Gene Regulation Is Determined Not Only by Sry but by Sex Chromosome Complement As Well

(2010) Patrick J. Wijchers et al.   DEVELOPMENTAL CELL

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates

(2010) Ziyang Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications

(2010) Anup Som et al.   PLoS One

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Parental Non-Equivalence of Imprinting Control Regions during Mammalian Development and Evolution

(2010) Reiner Schulz et al.   PLoS Genetics

Promoting the understanding of sex differences to enhance equity and excellence in biomedical science

(2010) Arthur P Arnold   Biology of Sex Differences

Sex Disparities in Cancer Incidence by Period and Age

(2009) M. B. Cook et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

(2009) J. Xu et al.   GENES & DEVELOPMENT

Sexual dimorphism in environmental epigenetic programming

(2009) Anne Gabory et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Genetic and molecular insights into the development and evolution of sexual dimorphism

(2009) Thomas M. Williams et al.   NATURE REVIEWS GENETICS

Downregulation of drs tumor suppressor gene in highly malignant human pulmonary neuroendocrine tumors

(2009) Shimakage   ONCOLOGY REPORTS

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

What does the “four core genotypes” mouse model tell us about sex differences in the brain and other tissues?

(2008) Arthur P. Arnold et al.   FRONTIERS IN NEUROENDOCRINOLOGY

An imputed genotype resource for the laboratory mouse

(2008) Jin P. Szatkiewicz et al.   MAMMALIAN GENOME

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH